Extracellular matrix/metastasis modifier genes for the prevention or inhibition of metastasis or growth of tumor and for characterization of tumor

Abstract

Disclosed are methods involving the administration of an extracellular matrix (ECM)/metastasis modifier gene, e.g., Anakin, Necdin, CentaurinD3 (CentD3), Csf1r, Brd4, Pi16, and Luc7l, for the prevention or inhibition of metastasis or of tumor growth. Further disclosed are methods of characterizing a tumor or cancer in a subject comprising detecting (i) a single nucleotide polymorphism (SNP) in an Anakin gene or a Brd4 gene of the subject, (ii) an amino acid substitution in an Anakin protein in the subject, or (iii) a level of expression of an Anakin gene or a Brd4 gene in the subject. Methods of screening a compound for anti-cancer activity and use of a compound with anti-cancer activity for the preparation of a medicament to treat or prevent cancer in a subject are also disclosed. Also disclosed is a method of inhibiting Sipa-1 in a subject.

1 . (canceled) 
     
     
         2 . A pharmaceutical composition comprising (i) a nucleic acid comprising a nucleotide sequence encoding a protein, (ii) a vector comprising the nucleic acid, (iii) a host cell comprising the vector, (iv) a gene product, or (v) a combination thereof, wherein the protein or gene product are encoded by a gene selected from the group consisting of: Anakin, Necdin, and Brd4, and a pharmaceutically acceptable carrier. 
     
     
         3 . The pharmaceutical composition of  claim 2 , wherein the nucleic acid comprises the nucleotide sequence of SEQ ID NO: 2 or 4. 
     
     
         4 . The pharmaceutical composition of  claim 2 , wherein the gene is an Anakin gene and the gene product is an Anakin protein or an Anakin mRNA. 
     
     
         5 . The pharmaceutical composition of  claim 4 , wherein the Anakin protein comprises the amino acid sequence of SEQ ID NO: 1 or 3. 
     
     
         6 . The pharmaceutical composition of  claim 2 , wherein the Necdin gene comprises the nucleotide sequence of SEQ ID NO: 10, or the Necdin gene product comprises the amino acid sequence of SEQ ID NO: 9. 
     
     
         7 . The pharmaceutical composition of  claim 2 , wherein the Brd4 gene comprises the nucleotide sequence of SEQ ID NO: 108 or 110, or the Brd4 gene product comprises the amino acid sequence of SEQ ID NO: 109 or 111. 
     
     
         8 . A method of preventing or inhibiting metastasis of a cancer cell in a subject comprising administering to the subject the pharmaceutical composition of  claim 2  in an amount that is effective to prevent or inhibit metastasis of the cancer cell in the subject. 
     
     
         9 . A pharmaceutical composition comprising (i) a nucleic acid comprising a nucleotide sequence encoding a protein, (ii) a vector comprising the nucleic acid, (iii) a host cell comprising the vector, (iv) a gene product, or (v) a combination thereof, wherein the protein or gene product are encoded by a gene selected from the group consisting of: CentaurinD3 (CentD3), Csf1r, Pi16, and Luc7l, and a pharmaceutically acceptable carrier. 
     
     
         10 . A method of preventing or inhibiting tumor growth in a subject comprising administering to the subject the pharmaceutical composition of  claim 2  in an amount that is effective to prevent or inhibit tumor growth in the subject. 
     
     
         11 . A method of characterizing a tumor or a cancer in a subject comprising detecting (i) a single nucleotide polymorphism (SNP) in an Anakin gene or a Brd4 gene of the subject, (ii) an amino acid substitution in an Anakin protein in the subject, or (iii) an expression level of an Anakin gene or a Brd4 gene in the subject, whereupon the tumor or cancer is characterized. 
     
     
         12 . The method of  claim 11 , wherein the tumor or cancer is characterized in terms of metastatic capacity, stage, tumor grade, nodal involvement, regional metastasis, distant metastasis, sex hormone receptor status, or tumor size. 
     
     
         13 . The method of  claim 12 , wherein the sex hormone receptor is the estrogen receptor or the progesterone receptor. 
     
     
         14 . The method of  claim 11 , wherein the SNP is located within an exon of an Anakin gene and results in an amino acid substitution. 
     
     
         15 . The method of  claim 14  wherein the amino acid substitution is a Leu substituted for a Pro at position 436 of SEQ ID NO: 1. 
     
     
         16 . The method of  claim 11 , wherein the SNP is a T→C at position 1421 of SEQ ID NO: 2. 
     
     
         17 . The method of  claim 11 , wherein the SNP is located within an intron of the Brd4 gene. 
     
     
         18 . The method of  claim 17 , wherein the SNP is an A→G at position 14290 of SEQ ID NO: 112, a G→A SNP at position 3185 of SEQ ID NO: 112, or a G→T SNP at position 13865 of SEQ ID NO: 112. 
     
     
         19 . The method of  claim 11 , wherein the subject is a mammal. 
     
     
         20 . The method of  claim 19 , wherein the mammal is a human. 
     
     
         21 . The method of  claim 11 , wherein the cancer is an epithelial cancer. 
     
     
         22 . The method of  claim 21 , wherein the epithelial cancer is breast cancer. 
     
     
         23 . The method of  claim 21 , wherein the epithelial cancer is renal cell carcinoma. 
     
     
         24 . The method of  claim 11 , wherein detecting a SNP comprises detecting a complementary SNP. 
     
     
         25 . The method of  claim 11 , wherein detecting a SNP comprises a polymerase chain reaction (PCR). 
     
     
         26 . The method of  claim 25 , wherein the PCR is carried out using primers and probes comprising the nucleotide sequences of SEQ ID NOs: 5 to 8. 
     
     
         27 . The method of  claim 11 , wherein the method is performed in vitro. 
     
     
         28 . The method of  claim 11 , wherein the method further comprises comparing (i) the nucleotide sequence of the Anakin gene or the Brd4 gene of the subject, (ii) the amino acid sequence of the Anakin protein of the subject, or (iii) the expression level of the Anakin gene or the Brd4 gene in the subject to a control. 
     
     
         29 . An isolated, purified, or synthetic nucleic acid comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 5 to 8. 
     
     
         30 . An isolated, purified, or synthetic antibody, or antigen binding portion thereof, which specifically binds to a murine Anakin protein or an Anakin allelic variant. 
     
     
         31 . The isolated, purified, or synthetic antibody, or antigen binding portion thereof, of  claim 30 , wherein the murine Anakin protein comprises the amino acid sequence of SEQ ID NO: 3. 
     
     
         32 . The isolated, purified, or synthetic antibody, or antigen binding portion thereof, of  claim 30 , wherein the Anakin allelic variant comprises the amino acid sequence of SEQ ID NO: 1 with an amino acid substitution of Leu to Pro at position 436 of SEQ ID NO: 1. 
     
     
         33 . The isolated, purified, or synthetic antibody, or antigen binding portion thereof, of  claim 30 , wherein the antibody, or antigen binding portion thereof, specifically binds to an epitope comprising Pro at position 436 of SEQ ID NO: 1 or Leu at position 436 of SEQ ID NO: 1. 
     
     
         34 . A kit comprising the antibody, or antigen binding portion thereof, of  claim 30 , or a nucleic acid which specifically hybridizes to a portion of a nucleic acid comprising a nucleotide sequence encoding an Anakin protein or Anakin allelic variant, or a combination thereof, and a set of user instructions. 
     
     
         35 . The kit of  claim 34 , wherein the nucleic acid comprising a nucleotide sequence encoding an Anakin protein comprises the nucleotide sequence of SEQ ID NO: 2 or 4. 
     
     
         36 . The kit of  claim 34 , wherein the nucleic acid comprising a nucleotide sequence encoding an Anakin allelic variant comprises the nucleotide sequence of SEQ ID NO: 2 with a T→C single nucleotide polymorphism (SNP) at position 1421 of SEQ ID NO: 2. 
     
     
         37 . The kit of  claim 34 , comprising one or more of the nucleic acids comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 5 to 8. 
     
     
         38 . A method for screening a compound for anti-cancer activity comprising (a) providing a cell that (i) under-expression a nucleic acid comprising a nucleotide sequence encoding an Anakin protein or a Brd4 protein or (ii) comprises an Anakin or Brd4 allelic variant, (b) contacting the cell with a compound of interest, and (c) assaying for anti-cancer activity. 
     
     
         39 . (canceled) 
     
     
         40 . A method of inhibiting Sipa-1 in a subject in need thereof comprising administering to the subject an effective amount of (i) a nucleic acid comprising a nucleotide sequence encoding an Anakin protein, (ii) a vector comprising the nucleic acid, (iii) a host cell comprising the vector, (iv) an Anakin gene product, or (v) a combination thereof. 
     
     
         41 . The method of  claim 40 , wherein the nucleic acid comprises the nucleotide sequence of SEQ ID NO: 2 or 4. 
     
     
         42 . The method of  claim 40 , wherein the Anakin gene product is a protein or an mRNA. 
     
     
         43 . The method of  claim 42 , wherein the protein comprises the amino acid sequence of SEQ ID NO: 1 or 3. 
     
     
         44 . The method of  claim 40 , wherein the method effectively inhibits Sipa-1 GTPase activity.